Overview

  • Introduction to IGV.
    • What is IGV.
    • How to run IGV.
  • Navigating IGV.
    • The IGV user interface.
    • Moving around genomes.
  • Loading and visualising data.
    • Genome information and annotation.
    • User supplied data.
    • Sample information.
    • External data.
  • Displaying genomics data
    • Basic visualisation.
    • Data dependent visualisation.

How to run IGV?

  • Requires Java
  • IGV available from Broad

igv

http://www.broadinstitute.org/software/igv/download

How to run IGV? (Webstart)

igv

  • Runs from webstart.
  • Always runs latest version of IGV

IGV GUI

.pull-left[ ] .pull-right[ - Sample information panel <1> - Genome Navigation panel <2> - Data panel <3> - Attribute panel <4>] — ## Menu bar

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  • File - Load data/sample information.
  • Genome - Load and manage genomes.
  • View - Display preferences.
  • Tracks - Group/sort/filter data tracks.
  • Regions - Create region/gene lists.
  • Tools - Access to Integrated tools (IGVtools/Bedtools).
  • GenomeSpace - Export/import from Genomespace

Moving around genomes

Scrolling

Jump to region.

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“Bookmarking” regions of interest

  • Regions may be added to “Regions of interest”

  • These act as bookmarks for areas of particular interest

  • Bookmarks can be added by -
    • Bookmarking visible window
    • Selecting region within window

Bookmarking - Visible window

.pull-left[ ] .pull-right[ ]

Bookmarking

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Bookmarking

  • Bookmarks may be created from selecting “region of interest” button and edge of region

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Sequences from regions of interest

  • A useful feature of “regions of interest” is to retrieve of BLAT sequences.

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Sequences from regions of interest

  • BLAT results present as table of hits.

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Viewing sequences

  • At a predefined resolution, sequence information becomes available.

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Viewing sequences

  • Strand of sequence can be altered.
  • Differing translation tables can be selected

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Sequences from regions of interest

  • A useful feature of “regions of interest” is to retrieve of BLAT sequences.

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Loading Genome Information

  • Most genomes can be selected from dropdown.

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Loading Genome Information

  • For supported genomes, gene positions are automatically included in “feature” panel.
  • Additional gene positions can be loaded into IGV in gff format

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Loading Sample Metadata

.pull-left[ - IGV allows the inclusion of information on samples. - Sample information is included in sample information panel.] .pull-right[ ] — ## Loading Sample Metadata

Example Sample information file http://www.broadinstitute.org/igvdata/exampleFiles/exampleSampleInfo.txt

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Using sample information.

  • Sample information can include discrete and continuous.

    • Can be used to “sort” and “filter” tracks.

    • Can split tracks across panels by “group”

Loading external data and annotation

** Load data from a URL ** - As with UCSC, IGV supports data hosted on external servers. - Data accessible from a URL such as HTTP and FTP can be loaded using the “Load from URL”.

Loading external data and annotation

** Load data from a server (IGV/Encode servers).**

  • Unlike UCSC, IGV comes with few external tracks.

  • External tracks (relevant to the genome) can be loaded from the IGV server or Encode-IGV server.

Grabbing encode data directly

  • Encode data can be downloaded from UCSC.
  • This however does not come with sample information provided through IGV interface

Viewing data

  • IGV associates common file formats with default display methods.

  • Most of the time IGV will make a sensible choice how we wish to display data.

Bed/bigBed

.pull-left[ - Basic - Tab-delimited - Chrom,Start,End - Bed6 - bigBed (recommended)] .pull-right[ igv

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Wig, BedGraph and BigWig

.pull-left[ - Wig/bedGraph require high memory load - Recommended format is bigWig] .pull-right[ igv

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BAM alignment files

.pull-left[ - BAM files contain alignment information. - Require an accompanying .bai index file for display] .pull-right[ igv

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Display preferences

** General **

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Display preferences

** Alignments **

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Track display options

** Graph/interval files** - Graph type

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Track display options

  • Autoscaling adjusts to track’s visible signal maximum

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IGV displays splicing.

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IGV - Overlay tracks

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Track summarisation.

IGV can be used to combine tracks

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Create new summed track

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